Sphinx Integration for Python Utilities

.github/workflows/embed-code-in-markdowns.yml

@@ -0,0 +1,17 @@
+name: Looping over values in Github Actions
+
+on:
+  push:
+
+jobs:
+  embed-code:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+
+      # - name: Collect Markdowns
+      #   id: collect-markdowns
+      #   run: |
+      #     files=$(find -name '*.md' -print)
+      #     echo "{MARKDOWN_FILES}=($files)" >> $GITHUB_ENV

.gitignore

@@ -7,3 +7,8 @@ __pycache__
 *.sublime-build
 *.pyc
 **/venv
+
+*env*
+*_build*
+*_static*
+*_templates*

LICENSE

@@ -0,0 +1,82 @@
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README.md

@@ -1,3 +1,35 @@
-![pre-processing](https://i.postimg.cc/Z5YJnS29/python-pre-processing.png)  
-![data analysis](https://i.postimg.cc/dQdsSnG0/python-data-analysis.png)  
-![explaratory data analysis](https://i.postimg.cc/CLghyD4s/python-explaratory-data-analysis.png)  
+# SPHINX Walkthrough
+
+This is a walkthrough of the SPHINX workflow. It is intended to be a quick reference guide. The python work used in this repository is based on a different repository and the credits for the code go to the original authors. The original repository can be found [here](https://github.com/cherkavi/python-utilities)
+
+## Setup
+
+The workflow is divided into 3 steps:
+
+1. Generate Markdowns for the python directory
+
+```bash
+
+# Preprocessing: Generate markdown files from the original scripts
+# In root directory,
+bash scripts/generate_markdown.sh doc/pages
+```
+
+2. To embed the code into markdown files, run the following command:
+
+```bash
+npm i -g markdown-autodocs
+markdown-autodocs -c code-block -o doc/pages/*
+```
+
+The package is also available as github action. The action can be found [here](https://github.com/marketplace/actions/markdown-autodocs).
+
+3.  To setup sphinx, run the following commands:
+
+```bash
+# In Ubuntu 20.04
+sudo apt-get install texlive texlive-latex-extra pandoc
+python3 -m pip install -r requirements.txt
+cd doc
+make html
+```

doc/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

doc/conf.py

@@ -0,0 +1,76 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+import os
+import sys
+
+# -- General Paths -----------------------------------------------------------
+
+sys.path.insert(0, os.path.abspath("../notebooks"))
+sys.path.insert(0, os.path.abspath(".."))
+
+# -- General configuration ---------------------------------------------------
+project = 'Python Utilities'
+copyright = '2022, Franklin Selva'
+author = 'Franklin Selva'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    "myst_parser",
+    "sphinx_rtd_theme",
+    "nbsphinx",
+    "nbsphinx_link",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.doctest",
+]
+
+source_suffix = {
+    ".rst": "restructuredtext",
+    ".md": "markdown",
+}
+
+templates_path = ['_templates']
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'sphinx_rtd_theme'
+html_theme_path = ["_themes", ]
+html_static_path = ['_static']
+
+html_theme_options = {
+    'logo_only': False,
+    'display_version': True,
+    'prev_next_buttons_location': 'bottom',
+    'style_external_links': False,
+    'vcs_pageview_mode': '',
+    'style_nav_header_background': '#2980B9',
+    # 'github_url': '',
+    # Toc options
+    'collapse_navigation': False,
+    'sticky_navigation': True,
+    'navigation_depth': 4,
+    'includehidden': True,
+    'titles_only': False
+}
+
+# -- Options for MystParser --------------------------------------------------
+
+# REFERENCE: https://myst-parser.readthedocs.io/en/latest/syntax/optional.html?highlight=anchor#auto-generated-header-anchors
+myst_heading_anchors = 3
+myst_enable_extensions = [
+    "linkify",
+]

doc/index.rst

@@ -0,0 +1,34 @@
+.. Python Utilities documentation master file, created by
+   sphinx-quickstart on Mon Nov  7 15:23:55 2022.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to Python Utilities's documentation!
+============================================
+
+.. https://www.sphinx-doc.org/en/master/usage/restructuredtext/directives.html
+
+.. include:: introduction.rst
+
+Table of Contents
+------------------
+
+* :ref:`python`
+* :ref:`jupyter`
+* :ref:`markdown`
+* :ref:`license`
+
+
+.. https://www.sphinx-doc.org/en/master/usage/restructuredtext/roles.html
+
+.. toctree::
+   :maxdepth: 2
+   :glob:
+   :titlesonly:
+   :caption: Contents
+   :hidden:
+
+   python
+   jupyter
+   markdown
+   license

doc/introduction.rst

@@ -0,0 +1,5 @@
+Introduction
+------------
+
+.. include:: ../README.md
+    :parser: myst_parser.sphinx_

doc/jupyter.rst

@@ -0,0 +1,14 @@
+.. _jupyter:
+
+Jupyter Notebook
+----------------
+
+.. toctree::
+   :maxdepth: 1
+   :numbered:
+   :glob:
+   :titlesonly:
+   :caption: Contents:
+
+   notebooks/jupyter_cheatsheet.ipynb
+   notebooks/jupyter_introduction.ipynb

doc/license.rst

@@ -0,0 +1,6 @@
+.. _license:
+
+LICENSE
+=======
+
+.. include:: ../LICENSE

doc/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

doc/markdown.rst

@@ -0,0 +1,12 @@
+.. _markdown:
+
+Markdown Files
+==============
+
+.. toctree::
+   :maxdepth: 1
+   :glob:
+   :numbered:
+
+   markdown/index
+   markdown/*